sisl.io.openmx.omxSileOpenMX

class sisl.io.openmx.omxSileOpenMX[source]

Bases: SileOpenMX

OpenMX-input file

By supplying base you can reference files in other directories. By default the base is the directory given in the file name.

Parameters:
  • filename (str) – input file

  • mode (str, optional) – opening mode, default to read-only

  • base (str, optional) – base-directory to read output files from.

Examples

>>> omx = omxSileOpenMX("tmp/input.dat") # reads output files in 'tmp/' folder
>>> omx = omxSileOpenMX("tmp/input.dat", base=".") # reads output files in './' folder

When using this file in conjunction with the sgeom script while your input data-files are named input.dat, please do this:

sgeom input.dat{omx} output.xyz

which forces the use of the omx file.

Plotting

plot

Plotting functions for the omxSileOpenMX class.

plot.geometry([output, ...])

Calls read_geometry and creates a GeometryPlot from its output.

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file([filename, filename_base])

File of the current Sile

get(key[, default])

Retrieve keyword from the file

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_basis(*args, **kwargs)

Reads basis

read_geometry([output])

Returns Geometry object

read_lattice([output])

Reads lattice

type(label)

Return the type of the fdf-keyword

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Attributes

base_file

File of the current Sile

file

Return the current file name (without the directory prefix)

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

close()
dir_file(filename=None, filename_base='')

File of the current Sile

get(key, default=None)[source]

Retrieve keyword from the file

Parameters:
  • key (str) – the key to search for

  • default (optional) – if the key is not found, this will be the returned value (default to None)

Returns:

value – a real value a float (or if the default is of float), for an integer, an int is returned.

Return type:

the value of the key. If the key is a block, a `list is returned`, for

plot.geometry(output=False, *args, data_kwargs={}, axes=['x', 'y', 'z'], atoms=None, atoms_style=[], atoms_scale=1.0, atoms_colorscale=None, drawing_mode=None, bind_bonds_to_ats=True, points_per_bond=20, bonds_style={}, bonds_scale=1.0, bonds_colorscale=None, show_atoms=True, show_bonds=True, show_cell='box', cell_style={}, nsc=(1, 1, 1), atoms_ndim_scale=(16, 16, 1), bonds_ndim_scale=(1, 1, 10), dataaxis_1d=None, arrows=(), backend='plotly')

Calls read_geometry and creates a GeometryPlot from its output.

Parameters:
  • output (bool) – whether to read geometry from output files (default to read from the input file).

  • order ({'dat', 'omx'}) – the order of which to try and read the geometry. If order is present output is disregarded.

  • axes (Axes) – The axes to project the geometry to.

  • atoms (AtomsIndex) – The atoms to plot. If None, all atoms are plotted.

  • atoms_style (Sequence[AtomsStyleSpec]) – List of style specifications for the atoms. See the showcase notebooks for examples.

  • atoms_scale (float) – Scaling factor for the size of all atoms.

  • atoms_colorscale (Optional[Colorscale]) – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • drawing_mode (Literal['scatter', 'balls', None]) – The method used to draw the atoms.

  • bind_bonds_to_ats (bool) – Whether to display only bonds between atoms that are being displayed.

  • points_per_bond (int) – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.

  • bonds_style (StyleSpec) – Style specification for the bonds. See the showcase notebooks for examples.

  • bonds_scale (float) – Scaling factor for the width of all bonds.

  • bonds_colorscale (Optional[Colorscale]) – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.

  • show_atoms (bool) – Whether to display the atoms.

  • show_bonds (bool) – Whether to display the bonds.

  • show_cell (Literal['box', 'axes', False]) – Mode to display the cell. If False, the cell is not displayed.

  • cell_style (StyleSpec) – Style specification for the cell. See the showcase notebooks for examples.

  • nsc (tuple[int, int, int]) – Number of unit cells to display in each direction.

  • atoms_ndim_scale (tuple[float, float, float]) – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).

  • bonds_ndim_scale (tuple[float, float, float]) – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).

  • dataaxis_1d (Optional[Union[np.ndarray, Callable]]) – Only meaningful for 1D plots. The data to plot on the Y axis.

  • arrows (Sequence[AtomArrowSpec]) – List of arrow specifications to display. See the showcase notebooks for examples.

  • backend – The backend to use to generate the figure.

Return type:

GeometryPlot

See also

GeometryPlot

The plot class used to generate the plot.

read_geometry

The method called to get the data.

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters:

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_basis(*args, **kwargs)[source]

Reads basis

Parameters:
  • output (bool, optional) – whether to read lattice from output files (default to read from the input file).

  • order ({'dat', 'omx'}) – the order of which to try and read the lattice If order is present output is disregarded.

read_geometry(output=False, *args, **kwargs)[source]

Returns Geometry object

One can limit the tried files to only one file by passing only a single file ending.

Parameters:
  • output (bool) – whether to read geometry from output files (default to read from the input file).

  • order ({'dat', 'omx'}) – the order of which to try and read the geometry. If order is present output is disregarded.

Return type:

Geometry

read_lattice(output=False, *args, **kwargs)[source]

Reads lattice

One can limit the tried files to only one file by passing only a single file ending.

Parameters:
  • output (bool) – whether to read lattice from output files (default to read from the input file).

  • order ({'dat', 'omx'}) – the order of which to try and read the lattice. If order is present output is disregarded.

Return type:

Lattice

type(label)[source]

Return the type of the fdf-keyword

Parameters:

label (str) – the label to look-up

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters:

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.

property base_file

File of the current Sile

property file

Return the current file name (without the directory prefix)

plot

Plotting functions for the omxSileOpenMX class.